Biomedical Engineering Reference
In-Depth Information
GROMACS
http://www.gromacs.org/
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular
dynamics simulation package originally developed in an open source mode and
released under the GPL licence.
1.5.2.2 Macromolecular Docking
Predictive protein-protein docking (using the structures of the unbound proteins
as starting point) can be investigated using either full atomic-resolution or coarse-
grained, lower-resolution models. A sampling of current resources includes
Zdock
http://zdock.bu.edu/cgi/help.cgi
Performs a convolution of three-dimensional grid representations of the two compo-
nent proteins via translational fast Fourier transforms (FFTs) in order to maximize
the interaction score.
Hex
http://hex.loria.fr/
Represents each component (protein or DNA) using expansions of real orthogonal
spherical polar basis functions, allowing the use of FFT correlations to search both
translation and rotational space for optimal docking geometries.
Haddock
http://www.nmr.chem.uu.nl/haddock/
Minimizes a penalty function that additionally incorporates restraints based on
experimental data concerning interacting residues in the actual complex, as derived
for example from NMR, mutagenesis, or biochemical data.
P-tools/Attract
http://ptoolsdocking.sourceforge.net/
Energy minimization of the interaction energy using either atomic-level or coarse-
grained representations of the component proteins. Incorporates some protein
flexibility via the addition of collective coordinate descriptions or multicopy
representations of alternative loop conformations, for example.
1.5.2.3 Molecular Visualization Environments
Visual Molecular Dynamics (VMD)
http://www.ks.uiuc.edu/Research/vmd/
VMD is a molecular visualization environment for displaying, animating and ana-
lyzing large biomolecular systems using 3-D graphics and built-in TCL scripting.
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